SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier.

ABSTRACT:

Background

Gene homology type classification is required for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. Consequently, a large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic data sets, these tools require high memory and CPU usage, typically available only in computational clusters.

Findings

Here we present a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. SwiftOrtho uses long k-mers to speed up homology search, while using a reduced amino acid alphabet and spaced seeds to compensate for the loss of sensitivity due to long k-m

SUBMITTER: Hu X 

PROVIDER: S-EPMC6812468 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature